never flash in windows, way too many problems across the board for many people
DOS or if the motherboard as an onboard utility in the bios, though for the dos make sure you use a bootable DOS (either floppy, cd, or usb), the command line in windows is not a DOS environment meant for flashing
Every motherboard has its own BIOS software to allow you to flash from floppy or USB at boot. Typically, you will see this pop up during the BIOS screen upon boot. Better this way...you don't want the flash to bomb out on you mid-way.